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ABRomics-analysis : developing Metagenomic Workflows for National Antibiotic Resistance Surveillance Platform
No full textInternational audienceAntibiotic resistance (ABR) is a major global public health issue, recognized as an urgent priority by international institutions. Especially regarding the emergence and the global dissemination of multidrug-resistant bacteria (MDRB) and antibiotic resistance genes (ARGs), as they can spread widely across humans, animals and environmental domains.ABRomics-analysis is an online platform designed for tracking MDRB and ARGs from bacterial genomes and metagenomes. This platform aims to provide a tool for the surveillance and research in antimicrobial resistance in a One Health context. While ABRomics currently supports only genomic analyses, focusing on isolated bacterial genomes obtained through culture-based methods, the development of metagenomic workflows is underway.Metagenomics enables the direct analysis of all genetic material within a sample, bypassing the need for bacterial isolation. To harness this potential, we are developing three Galaxy workflows designed to extract different levels of information from metagenomic samples.The first workflow processes raw sequencing reads to generate an initial characterization of the sample’s resistome and taxonomic composition. It provides a rapid assessment of the antimicrobial resistance genes (ARGs) and microbial communities present in the sample.The second workflow focuses on gene-level analysis by assembling raw reads into contigs, enabling a more refined exploration of the resistome, taxonomic diversity, functional potential, and mobile genetic elements. This approach allows for a better understanding of the genetic context of resistance genes.The third workflow reconstructs Metagenome-Assembled Genomes (MAG), providing a genome-resolved view of the microbial community. Each MAG is classified by taxonomy and its resistome, mobilome, and functional annotations are determined.Together, these workflows aim to extend the functionalities of ABRomics beyond genomic surveillance, providing a comprehensive framework for the metagenomic surveillance of antimicrobial resistance.ABRomics-analysis is accessible at https://analysis.abromics.fr
Unveiling the link between phytoplankton molecular physiology and biogeochemical cycling via genome-scale modeling
No full textInternational audienceEarth system models (ESMs) highly simplify their representation of biological processes, leading to major uncertainty in the impacts of climate change. Despite a growing understanding of molecular networks from genomic data, describing how changing phytoplankton physiology affects biogeochemical processes remains elusive. Here, we embed genome-scale models within a state-of-the-art ESM to deliver an integrated understanding of how gradients of nutrients modulate the molecular physiology of various plankton. In particular, when applied to Prochlorococcus , we find that glycogen and lipid management can be interpreted in terms of acclimation to different environments. Generalized to other phytoplankton such as the diatom Thalassiosira , we estimate the production of 39 metabolites that constitute hot spots of dissolved organic carbon described by their amount of carbon produced and their diversity of associated metabolites in ESMs. This modeling approach shows how genome scale–enabled ESMs have the potential to advance our understanding of microbial ecosystem functioning in ocean biogeochemical processes
L'encre de la clinique : panorama historique des données médicales (XVIIIe - XXIe siècles): Conférence puis atelier sur les archives hospitalières au sein d'une formation pour cadres de santé.
No full textConférence sur l'histoire des données médicales, de leur gestion par les hôpitaux et les archivistes, puis atelier de travail autour d'un dossier patiente extrait des fonds d'archives de l'Asile de Villejuif.I. Les archives hospitalières : la structuration administrativeII. La vie sociale des données III. Focus : le dossier patientCas pour l'atelier : un dossier patiente de l'Asile de Villejui
Nitrate activates an MKK3 ‐dependent MAPK module via NLP transcription factors in Arabidopsis
No full textInternational audiencePlant responses to nutrient availability are critical for plant development and yield. Nitrate, the major form of nitrogen in most soils, serves as both a nutrient and signaling molecule. Nitrate itself triggers rapid, major changes in gene expression, especially via nodule inception (NIN)‐like protein (NLP) transcription factors, and stimulates protein phosphorylation. Mitogen‐activated protein kinase (MAPK)‐related genes are among the early nitrate‐responsive genes; however, little is known about their roles in nitrate signaling pathways. Here, we show that nitrate resupply to nitrogen‐depleted Arabidopsis ( Arabidopsis thaliana ) plants triggers, within minutes, an MAPK cascade that requires NLP‐dependent transcriptional induction of mitogen‐activated protein kinase kinase kinase 13 ( MAP3K13 ) and MAP3K14 and that the MAPK cascade is composed of MKK3 and likely C‐clade MAPKs (MPK1/2/7/14). Importantly, nitrate reductase‐deficient mutants exhibited nitrate‐induced MPK7 activities comparable to those observed in wild‐type plants, indicating that nitrate itself is the signal that stimulates the cascade. We show that the modified expression of MAP3K13 and MAP3K14 affects nitrate‐stimulated BT2 expression and modulates plant responses to nitrogen availability, such as nitrate uptake and senescence. Our finding that an MAPK cascade involving MAP3K13 and MAP3K14 functions in the complex regulatory network governing responses to nitrate availability will guide future strategies to optimize plant responses to nitrogen fertilization and nitrogen use efficiency
Nanopore adaptive sampling to identify the NLR gene family in melon (Cucumis melo L.)
No full textInternational audienceBackground Nanopore adaptive sampling (NAS) offers a promising approach for assessing genetic diversity in targeted genomic regions. Here we designed and validated an experiment to enrich a set of resistance genes in several melon cultivars as a proof of concept. ResultsUsing the same reference to guide read acceptance or rejection with NAS, we successfully and accurately reconstructed the 15 regions in two newly assembled ssp. melo genomes and in a third ssp. agrestis cultivar. We obtained fourfold enrichment regardless of the tested samples, but with some variations according to the enriched regions. The accuracy of our assembly was further confirmed by PCR in the agrestis cultivar. We discussed parameters that could influence the enrichment and accuracy of NAS generated assemblies.Conclusions Overall, we demonstrated that NAS is a simple and efficient approach for exploring complex genomic regions, such as clusters of Nucleotide-binding site leucine-rich repeat (NLR) resistance genes. These regions are characterized by containing a high number of copy number variations, presence-absence polymorphisms and repetitive elements. These features make accurate assembly challenging but are crucial to study due to their central role in plant immunity and disease resistance. This approach facilitates resistance gene characterization in a large number of individuals, as required when breeding new cultivars suitable for the agroecological transition.</div
Rapports de travail et institutions au temps du capitalisme marchand (1800-1848)
No full textInternational audienc
ChronoRoot 2.0: An Open AI-Powered Platform for 2D Temporal Plant Phenotyping
No full textThe analysis of plant developmental plasticity, including root system architecture, is fundamental to understanding plant adaptability and development, particularly in the context of climate change and agricultural sustainability. While significant advances have been made in plant phenotyping technologies, comprehensive temporal analysis of root development remains challenging, with most existing solutions providing either limited throughput or restricted structural analysis capabilities. Here, we present ChronoRoot 2.0, an integrated open-source platform that combines affordable hardware with advanced artificial intelligence to enable sophisticated temporal plant phenotyping. The system introduces several major advances, offering an integral perspective of seedling development: (i) simultaneous multi-organ tracking of six distinct plant structures, (ii) quality control through real-time validation, (iii) comprehensive architectural measurements including novel gravitropic response parameters, and (iv) dual specialized user interfaces for both architectural analysis and high-throughput screening. We demonstrate the system's capabilities through three use cases for Arabidopsis thaliana: characterization of circadian growth patterns under different light conditions, detailed analysis of gravitropic responses in transgenic plants, and high-throughput screening of etiolation responses across multiple genotypes. ChronoRoot 2.0 maintains its predecessor's advantages of low cost and modularity while significantly expanding its capabilities, making sophisticated temporal phenotyping more accessible to the broader plant science community. The system's open-source nature, combined with extensive documentation and containerized deployment options, ensures reproducibility and enables community-driven development of new analytical capabilities
Le Design Fiction : aborder avec créativité et responsabilité un futur complexe
No full textFNEGE 4International audienceThis article examines the impact of two distinct pilot pedagogical experiments based on Design Fiction, conducted in different educational contexts, to develop creative, critical and anticipatory skills in students. Focusing on responsible entrepreneurship in response to future crises, the two experiments show how Design Fiction can be used to prepare students for action in a world undergoing profound change. The results demonstrate a significant transformation in the understanding of creativity and the development of cross-disciplinary skills such as critical thinking, the perception of complexity and the ability to make responsible decisions in a future, uncertain and complex environment.Cet article examine l'impact de deux expérimentations pédagogiques pilotes distinctes basées sur le Design Fiction, menées dans des contextes éducatifs différents, afin de développer chez les étudiants des compétences créatives, critiques et anticipatrices. Les deux dispositifs, centrés sur l'entrepreneuriat responsable en réponse aux crises futures, montrent comment le Design Fiction peut être utilisé pour préparer les étudiants à agir dans un monde en profondes mutations. Les résultats démontrent une transformation significative dans l’appréhension de la créativité et le développement de compétences transversales telles la pensée critique, la perception de la complexité et la capacité à prendre des décisions responsables en environnement futur, incertain et complexe
Nitrogen concentration shapes the size structure and the functional diversity of phytoplankton communities in the southern Indian Ocean
No full textInternational audiencePhytoplankton are fundamental to marine ecosystems, biogeochemical cycling and climate regulation. Their community structure and productivity are shaped by biotic and abiotic factors, notably temperature and macronutrient concentrations. Climate change is altering ocean vertical stratification and nutrient dynamics, with complex and often poorly understood impacts on phytoplankton communities and global primary production. To contribute characterizing these relationships, we analysed planktonic community composition using 18S rRNA amplicon sequencing and imaging f low cytometry in the southern Indian Ocean across a strong environmental gradient from warm, stratified, N-depleted (but relativ ely P-repleted) waters in the north to cold, mixed, macronutrient-replete waters in the south. Phytoplankton composition and local diversity correlated primarily with temperature and macronutrient concentrations, but smaller cells (<3 μm) were less affected than larger ones (>3 μm). To disentangle the relative inf luence of temperature and macronutrients, we applied a model of dissolved macronutrient diffusion, suggesting that nutrient limitation, primarily nitrogen, likely c onstrains the growth of osmotrophic phytoplankton with cell sizes exceeding 2-15 μm in the nutrient-depleted region. We show that smaller cells, with higher surface area-to-volume ratios, are likely to evade this limitation, explaining their lower sensitivity to nitrogen concentrations, both in their taxonomic composition and diversity. Imaging f low cytometry confirmed that larger cells persisting in nitrogen-depleted waters predominantly employ alternative nitrogen acquisition strategies such as diazotrophy or mixotrophy, fostering functional local diversity. Notably, three Prymnesiophyceae taxa exhibited partial limitation by nitrogen diffusion, raising questions about their potential for mixotrophy or diazotrophy, akin to Braarudosphaera bigelowii. Other environmental factors, such as trace metal concentrations, showed weaker corr elations with community structure metrics. Overall, our results are consistent with N concentration gradients and N:P imbalances driving a great share of planktonic diversity by constraining large-cell nutrient acquisition strategies and fostering functional diversification in oligotrophic regions of the Ocean.</div
Destinées ouvrières. Enquête sur les trajectoires socioprofessionelles d'ouvriers à Grenoble pendant l'industrialisation (1845-1939)
No full textThis thesis examines the dynamics of the formation of the Grenoble working class between the 1840s and the Second World War. During this period, Grenoble's industrial fabric underwent two waves of industrialisation, first in glove-making and then in metallurgy. These changes were reflected in the city's urban fabric, which underwent substantial development and saw the emergence of the industrial district of Saint-Bruno to the west of the city.Against this changing backdrop, we seek to analyse the driving forces behind proletarianisation by focusing on two elite groups of workers: glove-makers and metalworkers. By using different generational cohorts, we are reconstructing a set of individual socio-professional trajectories. This investigation allows us to explore two major questions: what does it mean to belong to the working class? What is an industrial town?We show that Grenoble's workers form a ‘sieve class’ that is subject to multiple forms of mobility (spatial, occupational and social), and that is fed by the gradual aggregation of various working populations. In the collective glove factory or in the metallurgical industrial district, stability (generational or intergenerational) in the trade is relative. These productive configurations, in a buoyant economic context, create opportunities, particularly for the best-skilled workers, who are offered opportunities for professional and social mobility. Nevertheless, there are several common features that underpin the membership of the group: the relationship with the industrial town, social practices and social endogamy.Cette thèse interroge les dynamiques de formation de la classe ouvrière grenobloise entre les années 1840 et la Seconde Guerre mondiale. Dans l’intervalle, le tissu industriel de Grenoble connaît deux vagues d’industrialisation liées à la ganterie puis à la métallurgie. Ces évolutions se traduisent spatialement puisque le tissu urbain évolue de façon substantielle et voit naître le quartier industriel de Saint-Bruno à l’ouest de la ville.Dans ce contexte évolutif, nous cherchons à analyser les ressorts de la prolétarisation en prenant pour objet deux groupes ouvriers d’élite : les gantiers et les métallurgistes. En nous appuyant sur différentes cohortes générationnelles, nous reconstruisons un ensemble de trajectoires socio-professionnelles individuelles. Ce dispositif d’enquête nous permet d’explorer deux grandes questions : que signifie appartenir au monde ouvrier ? Qu’est-ce qu’une ville industrielle ?Nous montrons que les ouvriers grenoblois forment une classe passoire traversée par de multiples mobilités (spatiales, professionnelles, sociales), qui est nourrie par l’agrégation progressive de diverses populations laborieuses. Dans la fabrique collective gantière ou dans le district industriel métallurgique, la stabilité (générationnelle ou intergénérationnelle) dans le métier est relative. Ces configurations productives, dans un contexte économique porteur, sont vectrices d’opportunités, en particulier pour les ouvriers les mieux formés, qui se voient offrir des occasions de mobilités professionnelles et sociales. Néanmoins, un certain nombre de traits communs fondent l’appartenance au groupe : le rapport à la ville industrielle, les pratiques de sociabilité ou encore l’endogamie sociale